1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information

Batch	Index	Genotype	Time	Data Path	Region
1	tBHP_4_0	tBHP	4	202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101	region_0
1	tBHP_4_1	tBHP	4	202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101	region_1
1	PBS_4_0	PBS	4	202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101	region_2
1	PBS_4_1	PBS	4	202402021652_20240202MFisherBHP4hxm500VZG191x01_VMSC00101	region_3
2	PBS_24_0	PBS	24	202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201	region_0
2	PBS_24_1	PBS	24	202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201	region_1
2	tBHP_24_0	tBHP	24	202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201	region_2
2	tBHP_24_1	tBHP	24	202402021711_20240202MFisherBHP24hxm500VZG191x02_VMSC05201	region_3

1.2 Data Quality

1.2.1 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

1.2.2 Transcript Count Level

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 122328 cells across 8 samples.

Segmented Cell Count in each Samples

Sample Index	Cell Count
tBHP_4_1	20452
tBHP_4_0	18804
tBHP_24_1	18206
PBS_4_1	16603
PBS_24_1	13900
tBHP_24_0	13452
PBS_24_0	12141
PBS_4_0	8770

–>

2.2 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample, and exclude uncertaine cells by bootstrapping probability < 0.9.

2.2.1 Cell Type Spatial Map

2.2.2 Endothelia & Microglia Spatial Map

2.2.3 Cell Type Count Table

Cell Type Count

	PBS_24	PBS_4	tBHP_24	tBHP_4
Astrocyte	2139	1856	2827	3004
Endo	603	678	1021	989
L2/3 Glut	547	317	903	1290
L4/5 Glut	1385	733	2010	2090
L5 Glut	563	501	901	1162
L6 Glut	299	205	404	718
L6b Glut	922	611	1223	1325
Microglia	445	518	581	1099
OPC	398	433	534	842
Oligo	2095	2308	3535	3061
Peri	319	296	513	601
STR D1 GABA	430	1763	609	2901
STR D2 GABA	824	2362	1043	3660
TH Glut	1117	459	726	46

3.1 Data Mining for Ischemia & Hypoxia

We found the ischemia and hypoxia mouse gene list by searching public mouse genome database Mouse Genome Informatics (MGI). It provided related gene list by matching terms from validated resources, such as gene ontology pathways.

Overall, 94 genes are found by ischemia term, and 349 genes are found in hypoxia.

Among those, 30 genes are both in ischemia & hypoxia pathway, which are: Ccl2, Epo, Pgf, Aifm1, Aqp3, Bcl2, Casp9, Casr, Cav1, Cav3, Egr1, Hk2, Hyou1, Kcnj8, Kcnj11, Mir874, Ndnf, Nfe2l2, Nol3, Nppc, P2rx2, Pik3cb, Pink1, Ptk2b, Rest, Rock2, Stat3, Tigar, Trem2, Trp53.

3.1.1 Ischemia Gene List

Type	MGI.ID	Symbol	Name	Chr	Start	End	Build	Strand	Best.Match.Type	Best.Match	Match.Score
protein coding gene	MGI:98259	Ccl2	C-C motif chemokine ligand 2	11	81926403	81928278	GRCm39		Disease Ortholog	ischemia	4
protein coding gene	MGI:108224	Ccl12	C-C motif chemokine ligand 12	11	81992671	81994225	GRCm39		Disease Ortholog	ischemia	4
protein coding gene	MGI:106639	Mthfr	methylenetetrahydrofolate reductase	4	148123534	148144008	GRCm39		Disease Ortholog	ischemia	4
lncRNA gene	MGI:5595308	Cirpil	cardiac ischemia reperfusion associated p53 interacting lncRNA	5	111638797	111640250	GRCm39		Name	cardiac ischemia reperfusion associated p53 interacting lncRNA	3
QTL	MGI:3795764	Lsq1	loss of tissue after ischemia QTL 1	7	syntenic	NA	GRCm39	null	Name	loss of tissue after ischemia QTL 1	3
protein coding gene	MGI:108448	Angpt1	angiopoietin 1	15	42288119	42540373	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:96819	Anxa1	annexin A1	19	20350798	20368035	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:108052	Bcl2l2	BCL2-like 2	14	55120900	55125691	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:1339751	Csf3	colony stimulating factor 3 (granulocyte)	11	98592089	98594455	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:1859388	Dll4	delta like canonical Notch ligand 4	2	119156265	119166147	GRCm39		Disease Ortholog	limb ischemia (subterm of ischemia)	3
protein coding gene	MGI:95407	Epo	erythropoietin	5	137481282	137484078	GRCm39		Disease Ortholog	limb ischemia (subterm of ischemia)	3
protein coding gene	MGI:95412	Ercc1	excision repair cross-complementing rodent repair deficiency, complementation group 1	7	19079016	19090449	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:99253	Etv2	ets variant 2	7	30333041	30335277	GRCm39		Disease Ortholog	limb ischemia (subterm of ischemia)	3
protein coding gene	MGI:1891012	F12	coagulation factor XII (Hageman factor)	13	55565771	55574606	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:95515	Fgf1	fibroblast growth factor 1	18	38971726	39062525	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:95791	Got1	glutamic-oxaloacetic transaminase 1, soluble	19	43488191	43513044	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:96079	Hgf	hepatocyte growth factor	5	16758493	16825150	GRCm39		Disease Ortholog	limb ischemia (subterm of ischemia)	3
protein coding gene	MGI:96244	Hspa1a	heat shock protein 1A	17	35188335	35191132	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:99517	Hspa1b	heat shock protein 1B	17	35175412	35178214	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:96432	Igf1	insulin-like growth factor 1	10	87694127	87772904	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:96547	Il1rn	interleukin 1 receptor antagonist	2	24226872	24241503	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:96949	Mdk	midkine	2	91760149	91762348	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:1929865	Nampt	nicotinamide phosphoribosyltransferase	12	32870334	32903368	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:97362	Nos3	nitric oxide synthase 3, endothelial cell	5	24569808	24589472	GRCm39		Disease Ortholog	limb ischemia (subterm of ischemia)	3
protein coding gene	MGI:105095	Pgf	placental growth factor	12	85213411	85224559	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:1860488	Proz	protein Z, vitamin K-dependent plasma glycoprotein	8	13110914	13126026	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:98278	Sele	selectin, endothelial cell	1	163875773	163885246	GRCm39		Disease Ortholog	brain ischemia (subterm of ischemia)	3
protein coding gene	MGI:108080	Serpinf1	serine (or cysteine) peptidase inhibitor, clade F, member 1	11	75300855	75313449	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:98351	Sod1	superoxide dismutase 1, soluble	16	90017650	90023221	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:1095418	Tfpi	tissue factor pathway inhibitor	2	84263199	84307119	GRCm39		Disease Ortholog	transient cerebral ischemia (subterm of ischemia)	3
protein coding gene	MGI:1926116	Abraxas2	BRISC complex subunit	7	132460954	132486840	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1349419	Aifm1	apoptosis-inducing factor, mitochondrion-associated 1	X	47563821	47602440	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1333777	Aqp3	aquaporin 3	4	41092724	41098183	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:88138	Bcl2	B cell leukemia/lymphoma 2	1	106465908	106642004	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:88139	Bcl2l1	BCL2-like 1	2	152622588	152673648	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1346013	Bves	blood vessel epicardial substance	10	45211868	45248575	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:88256	Camk2a	calcium/calmodulin-dependent protein kinase II alpha	18	61058704	61121224	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1277950	Casp9	caspase 9	4	141520923	141543287	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1351351	Casr	calcium-sensing receptor	16	36314058	36382503	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:102709	Cav1	caveolin 1, caveolae protein	6	17306387	17341323	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:107570	Cav3	caveolin 3	6	112436466	112449833	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1344418	Cib1	calcium and integrin binding 1	7	79876904	79882553	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1914829	Cpeb4	cytoplasmic polyadenylation element binding protein 4	11	31822211	31885634	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1339753	Csf1	colony stimulating factor 1 (macrophage)	3	107648364	107667785	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1339758	Csf1r	colony stimulating factor 1 receptor	18	61238644	61264211	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1097153	Cx3cl1	C-X3-C motif chemokine ligand 1	8	95498808	95509055	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1333815	Cx3cr1	C-X3-C motif chemokine receptor 1	9	119877749	119897362	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1195261	Eef2k	eukaryotic elongation factor-2 kinase	7	120442080	120506441	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:95295	Egr1	early growth response 1	18	34994260	34998009	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1919643	Faim2	Fas apoptotic inhibitory molecule 2	15	99394893	99426046	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:95713	Gja1	gap junction protein, alpha 1	10	56253297	56266519	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:95720	Gjb2	gap junction protein, beta 2	14	57336059	57342159	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1354372	Gpr31b	G protein-coupled receptor 31, D17Leh66b region	17	13270208	13271167	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:96103	Hk1	hexokinase 1	10	62104634	62215687	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1315197	Hk2	hexokinase 2	6	82702006	82751435	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:108030	Hyou1	hypoxia up-regulated 1	9	44290840	44303662	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1100508	Kcnj8	potassium inwardly-rectifying channel, subfamily J, member 8	6	142510563	142517340	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:107501	Kcnj11	potassium inwardly rectifying channel, subfamily J, member 11	7	45746545	45750215	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1346867	Map2k2	mitogen-activated protein kinase kinase 2	10	80941749	80960531	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1346868	Map2k3	mitogen-activated protein kinase kinase 3	11	60822880	60843637	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1346870	Map2k6	mitogen-activated protein kinase kinase 6	11	110289948	110416348	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1346876	Map3k5	mitogen-activated protein kinase kinase kinase 5	10	19810218	20018499	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:99458	Mef2c	myocyte enhancer factor 2C	13	83652153	83815199	GRCm39		Process	response to ischemia	3
miRNA gene	MGI:3718564	Mir874	microRNA 874	13	58170939	58171014	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1928485	Mlycd	malonyl-CoA decarboxylase	8	120121617	120137841	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1915419	Ndnf	neuron-derived neurotrophic factor	6	65648595	65689307	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:108420	Nfe2l2	nuclear factor, erythroid derived 2, like 2	2	75505857	75534985	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1925938	Nol3	nucleolar protein 3 (apoptosis repressor with CARD domain)	8	106002777	106008571	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:97369	Nppc	natriuretic peptide type C	1	86594015	86598295	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:97373	Npr3	natriuretic peptide receptor 3	15	11839982	11907287	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:103187	Nqo1	NAD(P)H dehydrogenase, quinone 1	8	108114857	108129838	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:2665170	P2rx2	purinergic receptor P2X, ligand-gated ion channel, 2	5	110487678	110491078	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1338859	P2rx4	purinergic receptor P2X, ligand-gated ion channel 4	5	122845607	122867801	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1860055	Panx1	pannexin 1	9	14917081	14956774	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1890615	Panx2	pannexin 2	15	88943937	88957770	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1195265	Per2	period circadian clock 2	1	91343704	91387046	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1922019	Pik3cb	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	9	98920455	99022264	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1916193	Pink1	PTEN induced putative kinase 1	4	138040720	138053618	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:2145814	Ppif	peptidylprolyl isomerase F (cyclophilin F)	14	25694578	25700892	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:104908	Ptk2b	PTK2 protein tyrosine kinase 2 beta	14	66390706	66518501	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1890564	Rcan1	regulator of calcineurin 1	16	92188839	92263057	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:103290	Rela	v-rel reticuloendotheliosis viral oncogene homolog A (avian)	19	5687511	5698158	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:104897	Rest	RE1-silencing transcription factor	5	77413338	77434279	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:107926	Rock2	Rho-associated coiled-coil containing protein kinase 2	12	16944896	17037824	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1915596	Sirt5	sirtuin 5	13	43518972	43548679	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:107996	Slc8a2	solute carrier family 8 (sodium/calcium exchanger), member 2	7	15863751	15894988	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1933154	Slc26a5	solute carrier family 26, member 5	5	22015653	22070602	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:98354	Sos1	SOS Ras/Rac guanine nucleotide exchange factor 1	17	80701181	80787882	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:107931	Sqstm1	sequestosome 1	11	50090193	50101654	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:103038	Stat3	signal transducer and activator of transcription 3	11	100777632	100830447	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:2442752	Tigar	Trp53 induced glycolysis regulatory phosphatase	6	127062079	127086520	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:1913150	Trem2	triggering receptor expressed on myeloid cells 2	17	48653429	48659304	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:98834	Trp53	transformation related protein 53	11	69471185	69482699	GRCm39		Process	response to ischemia	3
protein coding gene	MGI:103149	Uchl1	ubiquitin carboxy-terminal hydrolase L1	5	66833464	66844577	GRCm39		Process	response to ischemia	3

3.1.2 Hypoxia Gene List

Type	MGI.ID	Symbol	Name	Chr	Start	End	Build	Strand	Best.Match.Type	Best.Match	Match.Score
protein coding gene	MGI:106918	Hif1a	hypoxia inducible factor 1, alpha subunit	12	73948149	73994304	GRCm39		Name	hypoxia inducible factor 1, alpha subunit	3
protein coding gene	MGI:2442345	Hif1an	hypoxia-inducible factor 1, alpha subunit inhibitor	19	44551293	44564713	GRCm39		Name	hypoxia-inducible factor 1, alpha subunit inhibitor	3
protein coding gene	MGI:1859778	Hif3a	hypoxia inducible factor 3, alpha subunit	7	16765432	16796352	GRCm39		Name	hypoxia inducible factor 3, alpha subunit	3
protein coding gene	MGI:1916823	Hilpda	hypoxia inducible lipid droplet associated	6	29272487	29275445	GRCm39		Name	hypoxia inducible lipid droplet associated	3
protein coding gene	MGI:108030	Hyou1	hypoxia up-regulated 1	9	44290840	44303662	GRCm39		Name	hypoxia up-regulated 1	3
protein coding gene	MGI:1932286	Egln1	egl-9 family hypoxia-inducible factor 1	8	125635326	125676063	GRCm39		Name	egl-9 family hypoxia-inducible factor 1	3
protein coding gene	MGI:1932287	Egln2	egl-9 family hypoxia-inducible factor 2	7	26858083	26866227	GRCm39		Name	egl-9 family hypoxia-inducible factor 2	3
protein coding gene	MGI:1932288	Egln3	egl-9 family hypoxia-inducible factor 3	12	54225767	54250646	GRCm39		Name	egl-9 family hypoxia-inducible factor 3	3
protein coding gene	MGI:3845761	Methig1	methyltransferase hypoxia inducible domain containing 1	15	100251081	100282316	GRCm39		Name	methyltransferase hypoxia inducible domain containing 1	3
protein coding gene	MGI:109169	Epas1	endothelial PAS domain protein 1	17	87061292	87140838	GRCm39		Synonym	hypoxia inducible transcription factor 2alpha	3
protein coding gene	MGI:1930666	Higd1a	HIG1 domain family, member 1A	9	121677623	121686862	GRCm39		Protein Domain	Hypoxia induced protein, domain	3
protein coding gene	MGI:1922939	Higd1b	HIG1 domain family, member 1B	11	102726675	102728866	GRCm39		Protein Domain	Hypoxia induced protein, domain	3
protein coding gene	MGI:2685767	Higd1c	HIG1 domain family, member 1C	15	100262466	100281836	GRCm39		Protein Domain	Hypoxia induced protein, domain	3
protein coding gene	MGI:1914294	Higd2a	HIG1 domain family, member 2A	13	54738044	54738960	GRCm39		Protein Domain	Hypoxia induced protein, domain	3
protein coding gene	MGI:88574	Cybb	cytochrome b-245, beta polypeptide	X	9301493	9354005	GRCm39		Process	hypoxia-inducible factor-1alpha signaling pathway	3
protein coding gene	MGI:1921693	P4htm	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	9	108456061	108474866	GRCm39		Function	hypoxia-inducible factor-proline dioxygenase activity	3
protein coding gene	MGI:1926119	Pdk1	pyruvate dehydrogenase kinase, isoenzyme 1	2	71703568	71734202	GRCm39		Process	hypoxia-inducible factor-1alpha signaling pathway	3
protein coding gene	MGI:2384308	Pdk3	pyruvate dehydrogenase kinase, isoenzyme 3	X	92808213	92875807	GRCm39		Process	hypoxia-inducible factor-1alpha signaling pathway	3
protein coding gene	MGI:103223	Vhl	von Hippel-Lindau tumor suppressor	6	113600955	113608595	GRCm39		Process	hypoxia-inducible factor-1alpha signaling pathway	3
protein coding gene	MGI:109474	Commd1	COMM domain containing 1	11	22849728	22934539	GRCm39		Subterm Process	negative regulation of hypoxia-inducible factor-1alpha signaling pathway (hypoxia-inducible factor-1alpha signaling pathway)	3
protein coding gene	MGI:1920420	Rwdd3	RWD domain containing 3	3	120949047	120965344	GRCm39		Subterm Process	positive regulation of hypoxia-inducible factor-1alpha signaling pathway (hypoxia-inducible factor-1alpha signaling pathway)	3
protein coding gene	MGI:2443582	Abat	4-aminobutyrate aminotransferase	16	8331293	8439432	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97570	Abcb1a	ATP-binding cassette, sub-family B member 1A	5	8710077	8798575	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1352630	Abcc9	ATP-binding cassette, sub-family C member 9	6	142533588	142648041	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1098623	Acaa2	acetyl-CoA acyltransferase 2	18	74912283	74939278	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:87874	Ace	angiotensin I converting enzyme	11	105858774	105880790	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2159605	Acot2	acyl-CoA thioesterase 2	12	84034635	84040647	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1338946	Acvrl1	activin A receptor, type II-like 1	15	101026403	101043217	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87916	Ada	adenosine deaminase	2	163568504	163592159	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107825	Adam8	a disintegrin and metallopeptidase domain 8	7	139558845	139572475	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1333882	Adam15	ADAM metallopeptidase domain 15	3	89246947	89257589	GRCm39		Process	response to hypobaric hypoxia	3
protein coding gene	MGI:1096335	Adam17	a disintegrin and metallopeptidase domain 17	12	21373510	21423633	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:106675	Adipoq	adiponectin, C1Q and collagen domain containing	16	22965286	22976718	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108058	Adm	adrenomedullin	7	110226868	110229027	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2685083	Ado	2-aminoethanethiol dioxygenase	10	67380341	67384785	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:99401	Adora1	adenosine A1 receptor	1	134126963	134163169	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87938	Adrb2	adrenergic receptor, beta 2	18	62310887	62313030	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:103202	Adsl	adenylosuccinate lyase	15	80832691	80855147	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:893592	Ager	advanced glycosylation end product-specific receptor	17	34816836	34819910	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87965	Agtr1b	angiotensin II receptor, type 1b	3	20368637	20421341	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1339977	Agtrap	angiotensin II, type I receptor-associated protein	4	148161518	148172488	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1349419	Aifm1	apoptosis-inducing factor, mitochondrion-associated 1	X	47563821	47602440	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1341886	Ajuba	ajuba LIM protein	14	54804929	54815015	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87979	Ak4	adenylate kinase 4	4	101276474	101324192	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:87986	Akt1	thymoma viral proto-oncogene 1	12	112620260	112641266	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:96853	Alad	aminolevulinate, delta-, dehydratase	4	62427406	62438155	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87990	Alas2	aminolevulinic acid synthase 2, erythroid	X	149330443	149353614	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1353451	Aldh3a1	aldehyde dehydrogenase family 3, subfamily A1	11	61099336	61109244	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2144489	Alkbh5	alkB homolog 5, RNA demethylase	11	60428509	60449338	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88022	Ang	angiogenin, ribonuclease, RNase A family, 5	14	51328607	51339462	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104984	Ang2	angiogenin, ribonuclease A family, member 2	14	51432781	51436400	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1201793	Ang3	angiogenin, ribonuclease A family, member 3	14	syntenic	NA	GRCm39	null	Process	response to hypoxia	3
protein coding gene	MGI:2656551	Ang4	angiogenin, ribonuclease A family, member 4	14	52001349	52011047	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:3528599	Ang5	angiogenin, ribonuclease A family, member 5	14	44194526	44200537	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:3528602	Ang6	angiogenin, ribonuclease A family, member 6	14	44239121	44243875	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1202890	Angpt2	angiopoietin 2	8	18740279	18791578	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1336887	Angpt4	angiopoietin 4	2	151753130	151787257	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1888999	Angptl4	angiopoietin-like 4	17	33993874	34000549	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1306796	Apaf1	apoptotic peptidase activating factor 1	10	90825173	90918632	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:103201	Aqp1	aquaporin 1	6	55313417	55325540	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1333777	Aqp3	aquaporin 3	4	41092724	41098183	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:88071	Arnt	aryl hydrocarbon receptor nuclear translocator	3	95341699	95404551	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107188	Arnt2	aryl hydrocarbon receptor nuclear translocator 2	7	83895486	84059201	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96920	Ascl2	achaete-scute family bHLH transcription factor 2	7	142520566	142523001	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109349	Atf2	activating transcription factor 2	2	73646853	73722983	GRCm39		Process	intrinsic apoptotic signaling pathway in response to hypoxia	3
protein coding gene	MGI:88096	Atf4	activating transcription factor 4	15	80139385	80141742	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:107202	Atm	ataxia telangiectasia mutated	9	53350449	53448040	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88108	Atp1b1	ATPase, Na+/K+ transporting, beta 1 polypeptide	1	164264678	164285924	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1924148	B3gat1	beta-1,3-glucuronyltransferase 1	9	26644813	26672646	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1096330	Bad	BCL2-associated agonist of cell death	19	6919229	6929267	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2181667	Bbc3	BCL2 binding component 3	7	16042318	16052130	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:88138	Bcl2	B cell leukemia/lymphoma 2	1	106465908	106642004	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1891828	Becn1	beclin 1, autophagy related	11	101179084	101193112	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1197009	Birc2	baculoviral IAP repeat-containing 2	9	7818228	7837065	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88177	Bmp2	bone morphogenetic protein 2	2	133394079	133404805	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88184	Bmyc	brain expressed myelocytomatosis oncogene	2	25596891	25597733	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:109326	Bnip3	BCL2/adenovirus E1B interacting protein 3	7	138492565	138511235	GRCm39		Process	intrinsic apoptotic signaling pathway in response to hypoxia	3
protein coding gene	MGI:1332659	Bnip3l	BCL2/adenovirus E1B interacting protein 3-like	14	67222688	67246326	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2442836	Brip1	BRCA1 interacting protein C-terminal helicase 1	11	85948964	86092019	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1341265	Camk2d	calcium/calmodulin-dependent protein kinase II, delta	3	126389951	126639975	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88259	Camk2g	calcium/calmodulin-dependent protein kinase II gamma	14	20784943	20844156	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88264	Capn2	calpain 2	1	182294825	182345173	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2447188	Car9	carbonic anhydrase 9	4	43507026	43513729	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96544	Casp1	caspase 1	9	5298517	5307281	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107739	Casp3	caspase 3	8	47070326	47092724	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1277950	Casp9	caspase 9	4	141520923	141543287	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1351351	Casr	calcium-sensing receptor	16	36314058	36382503	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:88271	Cat	catalase	2	103284249	103315498	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102709	Cav1	caveolin 1, caveolae protein	6	17306387	17341323	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107570	Cav3	caveolin 3	6	112436466	112449833	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1338013	Cbfa2t3	CBFA2/RUNX1 translocation partner 3	8	123351880	123425848	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88279	Cbl	Casitas B-lineage lymphoma	9	44054273	44145346	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:88285	Cbs	cystathionine beta-synthase	17	31831602	31856170	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:98259	Ccl2	C-C motif chemokine ligand 2	11	81926403	81928278	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108069	Ccna2	cyclin A2	3	36619014	36626299	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:106185	Ccr2	C-C motif chemokine receptor 2	9	123901987	123913594	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88323	Cd24a	CD24a antigen	10	43454433	43460261	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107474	Cd38	CD38 antigen	5	44026153	44069714	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104565	Cdkn1b	cyclin dependent kinase inhibitor 1B	6	134897364	134902476	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1261428	Chchd2	coiled-coil-helix-coiled-coil-helix domain containing 2	5	129910002	129916311	GRCm39		Process	regulation of cellular response to hypoxia	3
pseudogene	MGI:3649942	Chchd2-ps	coiled-coil-helix-coiled-coil-helix domain containing 2, pseudogene	4	148152488	148152949	GRCm39		Process	regulation of cellular response to hypoxia	3
protein coding gene	MGI:87888	Chrna4	cholinergic receptor, nicotinic, alpha polypeptide 4	2	180664104	180685339	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:87891	Chrnb2	cholinergic receptor nicotinic beta 2 subunit	3	89660755	89671939	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1914813	Ciao3	cytosolic iron-sulfur assembly component 3	17	25992750	26002306	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1306784	Cited2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	10	17598966	17601422	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1346342	Clca1	chloride channel accessory 1	3	144710298	144738537	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1329044	Cldn3	claudin 3	5	135015068	135016326	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88470	Comt	catechol-O-methyltransferase	16	18225636	18245602	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108442	Cpeb1	cytoplasmic polyadenylation element binding protein 1	7	80996774	81105207	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2442640	Cpeb2	cytoplasmic polyadenylation element binding protein 2	5	43390513	43447067	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1098296	Cpt1a	carnitine palmitoyltransferase 1a, liver	19	3372334	3435733	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88513	Cr1l	complement C3b/C4b receptor 1 like	1	194781019	194813878	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:88498	Crhr1	corticotropin releasing hormone receptor 1	11	104023681	104066349	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88515	Cryaa	crystallin, alpha A	17	31896905	31900704	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88516	Cryab	crystallin, alpha B	9	50662625	50667936	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2149481	Cygb	cytoglobin	11	116536421	116544887	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:88588	Cyp1a1	cytochrome P450, family 1, subfamily a, polypeptide 1	9	57595211	57611107	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1926218	Cysltr1	cysteinyl leukotriene receptor 1	X	105617952	105647285	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1917336	Cysltr2	cysteinyl leukotriene receptor 2	14	73263043	73286554	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1197015	Daxx	Fas death domain-associated protein	17	34128388	34134564	GRCm39		Process	negative regulation of cellular response to hypoxia	3
protein coding gene	MGI:1916469	Ddah1	dimethylarginine dimethylaminohydrolase 1	3	145464447	145600032	GRCm39		Process	negative regulation of cellular response to hypoxia	3
protein coding gene	MGI:1921997	Ddit4	DNA-damage-inducible transcript 4	10	59785497	59787592	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1345277	Ddr2	discoidin domain receptor family, member 2	1	169799876	169938331	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1306782	Dio3	deiodinase, iodothyronine type III	12	110245664	110247531	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1921256	Dnm1l	dynamin 1-like	16	16130094	16176823	GRCm39		Process	response to hypobaric hypoxia	3
protein coding gene	MGI:1261827	Dnmt3a	DNA methyltransferase 3A	12	3856007	3964443	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:94919	Dpp4	dipeptidylpeptidase 4	2	62160417	62242575	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99578	Drd1	dopamine receptor D1	13	54205202	54209677	GRCm39		Process	negative regulation of cellular response to hypoxia	3
protein coding gene	MGI:94924	Drd2	dopamine receptor D2	9	49251927	49319477	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1101357	Ece1	endothelin converting enzyme 1	4	137589548	137692540	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95283	Edn1	endothelin 1	13	42454952	42461466	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:105923	Ednra	endothelin receptor type A	8	78389658	78451081	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95295	Egr1	early growth response 1	18	34994260	34998009	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:103267	Eif4ebp1	eukaryotic translation initiation factor 4E binding protein 1	8	27750355	27765684	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95392	Eng	endoglin	2	32536607	32572681	GRCm39		Process	detection of hypoxia	3
protein coding gene	MGI:95393	Eno1	enolase 1, alpha non-neuron	4	150321178	150333336	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:3648653	Eno1b	enolase 1B, retrotransposed	18	48178402	48181446	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:1276116	Ep300	E1A binding protein p300	15	81470329	81536278	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98277	Epha4	Eph receptor A4	1	77343822	77491725	GRCm39		Process	negative regulation of cellular response to hypoxia	3
protein coding gene	MGI:95407	Epo	erythropoietin	5	137481282	137484078	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95413	Ercc2	excision repair cross-complementing rodent repair deficiency, complementation group 2	7	19115942	19129619	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95414	Ercc3	excision repair cross-complementing rodent repair deficiency, complementation group 3	18	32373357	32403206	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1354385	Ero1a	endoplasmic reticulum oxidoreductase 1 alpha	14	45520544	45556029	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:109325	F7	coagulation factor VII	8	13076034	13085809	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95479	Fabp1	fatty acid binding protein 1, liver	6	71176863	71182018	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1917436	Fam162a	family with sequence similarity 162, member A	16	35864214	35891931	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95558	Flt1	FMS-like tyrosine kinase 1	5	147498414	147662821	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1859252	Fmn2	formin 2	1	174329391	174650295	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1915905	Fndc1	fibronectin type III domain containing 1	17	7957401	8046134	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95574	Fos	FBJ osteosarcoma oncogene	12	85520664	85524047	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:102858	Fosl2	fos-like antigen 2	5	32293145	32315186	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1890081	Foxo3	forkhead box O3	10	42057841	42152691	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1919268	Fundc1	FUN14 domain containing 1	X	17422803	17438564	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108520	Fzd4	frizzled class receptor 4	7	89053574	89062341	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95634	Gad2	glutamic acid decarboxylase 2	2	22512262	22583889	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:107516	Gata6	GATA binding protein 6	18	11052510	11085636	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95781	Gnb1	guanine nucleotide binding protein (G protein), beta 1	4	155575818	155643726	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:109165	Gngt1	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	6	3993792	3997436	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95821	Grin2b	glutamate receptor, ionotropic, NMDA2B (epsilon 2)	6	135690231	136150509	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1315197	Hk2	hexokinase 2	6	82702006	82751435	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96163	Hmox1	heme oxygenase 1	8	75820249	75827217	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:109373	Hmox2	heme oxygenase 2	16	4544225	4584606	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109369	Hp1bp3	heterochromatin protein 1, binding protein 3	4	137943607	137971994	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:104720	Hsd11b2	hydroxysteroid 11-beta dehydrogenase 2	8	106245387	106250620	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98817	Hsp90b1	heat shock protein 90, beta (Grp94), member 1	10	86526705	86541308	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96542	Il1a	interleukin 1 alpha	2	129141530	129151892	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96552	Il3	interleukin 3	11	54156129	54158103	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107936	Il18	interleukin 18	9	50466127	50493140	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96570	Inhba	inhibin beta-A	13	16186436	16206206	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1928268	Ireb2	iron responsive element binding protein 2	9	54771073	54819814	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:96600	Itga2	integrin alpha 2	13	114969617	115068636	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96623	Itpr1	inositol 1,4,5-trisphosphate receptor 1	6	108190057	108528070	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99418	Itpr2	inositol 1,4,5-triphosphate receptor 2	6	146009797	146403721	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96662	Kcna5	potassium voltage-gated channel, shaker-related subfamily, member 5	6	126509514	126512375	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102663	Kcnd2	potassium voltage-gated channel, Shal-related family, member 2	6	21215502	21729804	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1100508	Kcnj8	potassium inwardly-rectifying channel, subfamily J, member 8	6	142510563	142517340	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107501	Kcnj11	potassium inwardly rectifying channel, subfamily J, member 11	7	45746545	45750215	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109366	Kcnk2	potassium channel, subfamily K, member 2	1	188940127	189134470	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1100509	Kcnk3	potassium channel, subfamily K, member 3	5	30745514	30782614	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:99923	Kcnma1	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	14	23342356	24055173	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1095419	Kdm6a	lysine (K)-specific demethylase 6A	X	18028814	18146175	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:96683	Kdr	kinase insert domain protein receptor	5	76093487	76139118	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104576	Lct	lactase	1	128212493	128256055	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104663	Lep	leptin	6	29060220	29073875	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96787	Lif	leukemia inhibitory factor	11	4207587	4222514	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1352502	Limd1	LIM domains containing 1	9	123307771	123350617	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96794	Lmna	lamin A	3	88388455	88413842	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1921392	Lonp1	lon peptidase 1, mitochondrial	17	56921297	56933887	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2137913	Loxl2	lysyl oxidase-like 2	14	69846517	69933283	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104797	Lta	lymphotoxin A	17	35422141	35424327	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1346866	Map2k1	mitogen-activated protein kinase kinase 1	9	64093066	64160887	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:96922	Mb	myoglobin	15	76899687	76934868	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96952	Mdm2	transformed mouse 3T3 cell double minute 2	10	117524780	117546663	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:99918	Mecp2	methyl CpG binding protein 2	X	73070198	73129296	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1914999	Mgarp	mitochondria localized glutamic acid rich protein	3	51295833	51303968	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2146020	Mief1	mitochondrial elongation factor 1	15	80118284	80137572	GRCm39		Process	cellular response to hypoxia	3
miRNA gene	MGI:3618742	Mir199a-2	microRNA 199a-2	1	162045383	162045492	GRCm39		Process	cellular response to hypoxia	3
miRNA gene	MGI:2676890	Mir214	microRNA 214	1	162050937	162051046	GRCm39		Process	cellular response to hypoxia	3
miRNA gene	MGI:3629905	Mir668	microRNA 668	12	109701166	109701231	GRCm39		Process	cellular response to hypoxia	3
miRNA gene	MGI:3718564	Mir874	microRNA 874	13	58170939	58171014	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1929514	Mlst8	MTOR associated protein, LST8 homolog (S. cerevisiae)	17	24692525	24698052	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97009	Mmp2	matrix metallopeptidase 2	8	93553920	93580049	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:101900	Mmp14	matrix metallopeptidase 14 (membrane-inserted)	14	54669055	54679913	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96080	Mst1	macrophage stimulating 1 (hepatocyte growth factor-like)	9	107957635	107962202	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95691	Mstn	myostatin	1	53100799	53107238	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97173	Mt3	metallothionein 3	8	94879235	94880774	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102504	mt-Co1	mitochondrially encoded cytochrome c oxidase I	MT	5328	6872	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102503	mt-Co2	mitochondrially encoded cytochrome c oxidase II	MT	7013	7696	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102501	mt-Cytb	mitochondrially encoded cytochrome b	MT	14145	15288	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:101787	mt-Nd1	mitochondrially encoded NADH dehydrogenase 1	MT	2751	3707	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102498	mt-Nd4	mitochondrially encoded NADH dehydrogenase 4	MT	10167	11544	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102496	mt-Nd5	mitochondrially encoded NADH dehydrogenase 5	MT	11742	13565	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1928394	Mtor	mechanistic target of rapamycin kinase	4	148533068	148642140	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97250	Myc	myelocytomatosis oncogene	15	61857240	61862223	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2137495	Myocd	myocardin	11	65067387	65160815	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1915419	Ndnf	neuron-derived neurotrophic factor	6	65648595	65689307	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:102570	Ndp	Norrie disease (pseudoglioma) (human)	X	16751760	16778013	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1341799	Ndrg1	N-myc downstream regulated gene 1	15	66801167	66841489	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97306	Nf1	neurofibromin 1	11	79230519	79472438	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:103296	Nfatc3	nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 3	8	106785472	106857169	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108420	Nfe2l2	nuclear factor, erythroid derived 2, like 2	2	75505857	75534985	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2151886	Ngb	neuroglobin	12	87144305	87149313	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97352	Nkx3-1	NK3 homeobox 1	14	69428141	69432107	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1925938	Nol3	nucleolar protein 3 (apoptosis repressor with CARD domain)	8	106002777	106008571	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:1855692	Nono	non-POU-domain-containing, octamer binding protein	X	100473080	100492199	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2154441	Nop53	NOP53 ribosome biogenesis factor	7	15671760	15680033	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97361	Nos2	nitric oxide synthase 2, inducible	11	78811613	78851052	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97363	Notch1	notch 1	2	26347914	26393834	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1101358	Npepps	aminopeptidase puromycin sensitive	11	97096668	97171464	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97369	Nppc	natriuretic peptide type C	1	86594015	86598295	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1352456	Nr4a2	nuclear receptor subfamily 4, group A, member 2	2	56996845	57014018	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1339639	Ogt	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)	X	100683666	100727957	GRCm39		Process	negative regulation of cellular response to hypoxia	3
protein coding gene	MGI:97438	Oprd1	opioid receptor, delta 1	4	131838037	131871797	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2665170	P2rx2	purinergic receptor P2X, ligand-gated ion channel, 2	5	110487678	110491078	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1097160	P2rx3	purinergic receptor P2X, ligand-gated ion channel, 3	2	84828927	84867806	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97464	P4hb	prolyl 4-hydroxylase, beta polypeptide	11	120451124	120464079	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1339975	Pak1	p21 (RAC1) activated kinase 1	7	97437748	97561588	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97501	Pck1	phosphoenolpyruvate carboxykinase 1, cytosolic	2	172994866	173001067	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1860611	Pdlim1	PDZ and LIM domain 1 (elfin)	19	40210683	40260060	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104629	Penk	preproenkephalin	4	4133536	4138815	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:105095	Pgf	placental growth factor	12	85213411	85224559	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97555	Pgk1	phosphoglycerate kinase 1	X	105230706	105247305	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:102520	Phb2	prohibitin 2	6	124689299	124693913	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1922019	Pik3cb	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	9	98920455	99022264	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:1346036	Pin1	peptidyl-prolyl cis/trans isomerase, NIMA-interacting 1	9	20563335	20575008	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:3649546	Pin1rt1	peptidyl-prolyl cis/trans isomerase, NIMA-interacting 1, retrogene 1	2	104544271	104546724	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1916193	Pink1	PTEN induced putative kinase 1	4	138040720	138053618	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:97610	Plat	plasminogen activator, tissue	8	23247743	23272860	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97611	Plau	plasminogen activator, urokinase	14	20886728	20893453	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:892877	Pld2	phospholipase D2	11	70430890	70448936	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2387630	Plekhn1	pleckstrin homology domain containing, family N member 1	4	156305913	156312999	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109604	Plk3	polo like kinase 3	4	116985852	116991160	GRCm39		Process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia	3
protein coding gene	MGI:99907	Plod1	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	4	147994210	148021224	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104662	Pml	promyelocytic leukemia	9	58125359	58157069	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1926321	Postn	periostin, osteoblast specific factor	3	54268530	54298458	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104740	Ppara	peroxisome proliferator activated receptor alpha	15	85619184	85687020	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:101884	Ppard	peroxisome proliferator activator receptor delta	17	28451715	28520446	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97747	Pparg	peroxisome proliferator activated receptor gamma	6	115337912	115467360	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97749	Ppia	peptidylprolyl isomerase A	11	6365867	6369817	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2145955	Prkaa1	protein kinase, AMP-activated, alpha 1 catalytic subunit	15	5173343	5211380	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97596	Prkcb	protein kinase C, beta	7	121888327	122233625	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97599	Prkce	protein kinase C, epsilon	17	86475213	86965347	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1206587	Prl4a1	prolactin family 4, subfamily a, member 1	13	28200195	28207531	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:894281	Prl8a2	prolactin family 8, subfamily a, member 2	13	27529656	27538199	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1316652	Prmt2	protein arginine N-methyltransferase 2	10	76043060	76073699	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109583	Pten	phosphatase and tensin homolog	19	32734977	32803560	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1097156	Ptgis	prostaglandin I2 (prostacyclin) synthase	2	167033725	167082524	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:97798	Ptgs2	prostaglandin-endoperoxide synthase 2	1	149975851	149983978	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:104908	Ptk2b	PTK2 protein tyrosine kinase 2 beta	14	66390706	66518501	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97830	Pygm	muscle glycogen phosphorylase	19	6434438	6448494	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108016	Rad21	RAD21 cohesin complex component	15	51825636	51855143	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97847	Raf1	v-raf-leukemia viral oncogene 1	6	115595530	115653596	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:97895	Reg1	regenerating islet-derived 1	6	78402966	78405651	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:104897	Rest	RE1-silencing transcription factor	5	77413338	77434279	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1913464	Rgcc	regulator of cell cycle	14	79526190	79539075	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:107926	Rock2	Rho-associated coiled-coil containing protein kinase 2	12	16944896	17037824	GRCm39		Process	regulation of cellular response to hypoxia	3
protein coding gene	MGI:104661	Rora	RAR-related orphan receptor alpha	9	68561068	69295528	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1921620	Rptor	regulatory associated protein of MTOR, complex 1	11	119493731	119790402	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1915835	Rtn4	reticulon 4	11	29642947	29694331	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:99659	Ryr1	ryanodine receptor 1, skeletal muscle	7	28702765	28824599	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99685	Ryr2	ryanodine receptor 2, cardiac	13	11567988	12121831	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2135958	Scap	SREBF chaperone	9	110162356	110214017	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1924233	Scfd1	Sec1 family domain containing 1	12	51424296	51496887	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98248	Scn2a	sodium channel, voltage-gated, type II, alpha	2	65451115	65597791	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1914175	Sdhd	succinate dehydrogenase complex, subunit D, integral membrane protein	9	50507657	50515112	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:892014	Sfrp1	secreted frizzled-related protein 1	8	23901518	23939648	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2135607	Sirt1	sirtuin 1	10	63154784	63174814	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1927664	Sirt2	sirtuin 2	7	28466192	28488086	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1922637	Sirt4	sirtuin 4	5	115616069	115622784	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:95755	Slc2a1	solute carrier family 2 (facilitated glucose transporter), member 1	4	118965942	118994527	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:95758	Slc2a4	solute carrier family 2 (facilitated glucose transporter), member 4	11	69833365	69839014	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1860103	Slc2a8	solute carrier family 2, (facilitated glucose transporter), member 8	2	32863002	32872095	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:96285	Slc6a4	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	11	76889429	76923166	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107956	Slc8a1	solute carrier family 8 (sodium/calcium exchanger), member 1	17	81680534	82045806	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:107976	Slc8a3	solute carrier family 8 (sodium/calcium exchanger), member 3	12	81244689	81379954	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:102462	Slc9a1	solute carrier family 9 (sodium/hydrogen exchanger), member 1	4	133097022	133151013	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1345279	Slc11a2	solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2	15	100285779	100322090	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1927073	Slc29a1	solute carrier family 29 (nucleoside transporters), member 1	17	45896126	45910532	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1201674	Smad3	SMAD family member 3	9	63554049	63665276	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:894293	Smad4	SMAD family member 4	18	73772080	73836851	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98352	Sod2	superoxide dismutase 2, mitochondrial	17	13226726	13237006	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:103181	Sod3	superoxide dismutase 3, extracellular	5	52521146	52527080	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98366	Sox4	SRY (sex determining region Y)-box 4	13	29132902	29137682	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98397	Src	Rous sarcoma oncogene	2	157265828	157313758	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:106658	Srf	serum response factor	17	46859255	46867101	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:103038	Stat3	signal transducer and activator of transcription 3	11	100777632	100830447	GRCm39		Process	regulation of cellular response to hypoxia	3
protein coding gene	MGI:109131	Stc1	stanniocalcin 1	14	69266738	69278850	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1316731	Stc2	stanniocalcin 2	11	31309441	31320061	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1099440	Suv39h1	suppressor of variegation 3-9 1	X	7927410	7940999	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1890396	Suv39h2	suppressor of variegation 3-9 2	2	3456852	3476068	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1341163	Tacc3	transforming, acidic coiled-coil containing protein 3	5	33815472	33836339	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1351652	Tbl2	transducin (beta)-like 2	5	135178288	135192727	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:98664	Tek	TEK receptor tyrosine kinase	4	94627526	94763213	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1202709	Tert	telomerase reverse transcriptase	13	73775030	73797962	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:107810	Tfam	transcription factor A, mitochondrial	10	71061294	71074110	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98822	Tfrc	transferrin receptor	16	32427738	32451612	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98725	Tgfb1	transforming growth factor, beta 1	7	25386427	25404502	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:98726	Tgfb2	transforming growth factor, beta 2	1	186354989	186438186	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98727	Tgfb3	transforming growth factor, beta 3	12	86103519	86125815	GRCm39		Process	detection of hypoxia	3
protein coding gene	MGI:98735	Th	tyrosine hydroxylase	7	142446516	142453732	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2442752	Tigar	Trp53 induced glycolysis regulatory phosphatase	6	127062079	127086520	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:2139220	Tm9sf4	transmembrane 9 superfamily member 4	2	153003223	153052386	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99682	Tmbim6	transmembrane BAX inhibitor motif containing 6	15	99290828	99307930	GRCm39		Process	negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:104798	Tnf	tumor necrosis factor	17	35418357	35420983	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1913150	Trem2	triggering receptor expressed on myeloid cells 2	17	48653429	48659304	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:98823	Trh	thyrotropin releasing hormone	6	92219042	92221631	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98834	Trp53	transformation related protein 53	11	69471185	69482699	GRCm39		Process	intrinsic apoptotic signaling pathway in response to hypoxia	3
protein coding gene	MGI:1926945	Trpv4	transient receptor potential cation channel, subfamily V, member 4	5	114760213	114796482	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:102548	Tsc2	TSC complex subunit 2	17	24814790	24851604	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98872	Twist1	twist basic helix-loop-helix transcription factor 1	12	34007670	34009828	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1929468	Txn2	thioredoxin 2	15	77799251	77813194	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1860276	Ubqln1	ubiquilin 1	13	58323970	58363467	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1932970	Ucn3	urocortin 3	13	3990688	3995349	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:109354	Ucp2	uncoupling protein 2 (mitochondrial, proton carrier)	7	100142565	100148832	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1099787	Ucp3	uncoupling protein 3 (mitochondrial, proton carrier)	7	100122198	100135639	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99542	Usf1	upstream transcription factor 1	1	171238875	171246327	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:1918722	Usp19	ubiquitin specific peptidase 19	9	108367806	108379536	GRCm39		Process	regulation of cellular response to hypoxia	3
protein coding gene	MGI:1346329	Uts2	urotensin 2	4	151081554	151086267	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2177651	Vasn	vasorin	16	4457805	4468666	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:103178	Vegfa	vascular endothelial growth factor A	17	46327919	46343295	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:106199	Vegfb	vascular endothelial growth factor B	19	6959841	6965019	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:109124	Vegfc	vascular endothelial growth factor C	8	54530567	54639489	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:108037	Vegfd	vascular endothelial growth factor D	X	163156374	163185646	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:98935	Vldlr	very low density lipoprotein receptor	19	27193884	27231631	GRCm39		Process	cellular response to hypoxia	3
protein coding gene	MGI:1915086	Wdr83	WD repeat domain containing 83	8	85801664	85807375	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:2141920	Wtip	WT1 interacting protein	7	33808968	33832693	GRCm39		Process	response to hypoxia	3
protein coding gene	MGI:99137	Xrcc1	X-ray repair complementing defective repair in Chinese hamster cells 1	7	24246124	24272863	GRCm39		Process	response to hypoxia	3
lncRNA gene	MGI:1916199	Zfas1	zinc finger, NFX1-type containing 1, antisense RNA 1	2	166904854	166907782	GRCm39		Process	regulation of hypoxia-induced intrinsic apoptotic signaling pathway	3
protein coding gene	MGI:107946	Zfp36l1	zinc finger protein 36, C3H type-like 1	12	80154534	80159787	GRCm39		Process	cellular response to hypoxia	3

3.2 Gene Differentiation Volcano

Here, we use Wilcoxon Test to compute gene differential expression (DE). The statistical significance was cut-off by log2(Fold Change) > 1 or log2(Fold Change) < -1 and p_value < 0.05.

The ischemia-related gene are highlighted in volcano plot by purple color, while hypoxia-related genes are marked in green. No ischemia-hypoxia-overlap gene is found in DE.

3.2.1 Microglia (4 hours), tBHP vs PBS

	logfoldchanges	pvals
Selplg	7.804862	0.0000000
Apoe	-3.794668	0.0000000
C1qa	3.027765	0.0000000
Slc17a7	1.934162	0.0001875
Serpinf1	-1.611794	0.0127633
Nnat	-1.523112	0.0002573
Ctss	1.202592	0.0003786
Cd9	-1.000260	0.0068657

3.2.2 Microglia(24 hours), tBHP vs PBS

	logfoldchanges	pvals
Tmem119	9.655052	0.0000000
Cx3cr1	9.207951	0.0000000
Csf1r	7.521422	0.0000000
C1qa	6.288658	0.0000000
Ctss	4.346459	0.0000035
Camk2a	3.978816	0.0000000
Bin1	2.346426	0.0000000
Apoe	1.898717	0.0000196
Ctsb	1.771201	0.0000000
Plp1	1.656879	0.0022404
Cd14	1.628826	0.0000000
Cspg5	1.620137	0.0000051
Aldh1l1	1.425023	0.0046848
Trem2	1.414192	0.0002061
Sncg	1.364001	0.0245285
Itgam	1.336048	0.0000000
Casp8	1.334647	0.0017914
Rbfox3	1.271873	0.0096435
Inpp5d	1.213771	0.0000029
Cd9	1.205624	0.0023450
Spi1	1.185843	0.0004712
Tcerg1	1.140319	0.0018037
Sla	1.096807	0.0000018
Zbtb20	1.081156	0.0009113
Nptx1	1.074096	0.0166972
Lrpprc	1.068678	0.0109181
Sharpin	1.065369	0.0195681
Abi3	1.056846	0.0000005
Syn1	1.051837	0.0025161
Ctsc	1.000470	0.0000616

3.2.3 Endothelial (4 hours), tBHP vs PBS

	logfoldchanges	pvals
Icam1	4.321182	0.0000005
Vcam1	1.990366	0.0359665
Slc17a7	1.944467	0.0000000
Agt	-1.849056	0.0004980
Nnat	-1.548581	0.0000001
Pecam1	1.424326	0.0000000
Nptxr	1.219218	0.0154648
Klf2	-1.188156	0.0000000
Cldn5	1.106118	0.0166088
Camk2a	1.005879	0.0001490

3.2.4 Endothelial (24 hours), tBHP vs PBS

	logfoldchanges	pvals
Bsg	14.207772	0.0000000
Cldn5	8.383662	0.0000000
Apoe	3.879512	0.0000000
Camk2a	3.245064	0.0000000
App	2.708132	0.0000033
Flt1	2.425270	0.0000000
Pecam1	2.256013	0.0000000
Mfsd2a	2.185250	0.0000000
Ctnnb1	1.970689	0.0000000
Gfap	1.806280	0.0000364
Kcnq1	1.715021	0.0091454
Plp1	1.607371	0.0013174
Cspg5	1.545747	0.0000000
Cx3cl1	1.531581	0.0000054
Nos3	1.520198	0.0000000
Xdh	1.502282	0.0000000
Nptxr	1.472057	0.0000195
Ppp1r1b	1.443743	0.0173912
Klf2	1.395932	0.0000000
Fn1	1.385187	0.0003460
Sema3g	1.272809	0.0486582
Arc	-1.256589	0.0003183
Stard8	1.242842	0.0001185
Zbtb20	1.223462	0.0000000
Rgs5	1.216236	0.0000001
Lef1	1.192588	0.0000001
Tcerg1	1.179086	0.0141037
Ngrn	1.148234	0.0371505
Cdh5	1.141593	0.0000000
Pcdhgc3	1.121873	0.0000000
Grb2	1.105423	0.0009515
Rbfox3	1.103138	0.0068434
Syn1	1.100524	0.0012414
Bin1	1.090345	0.0012565
Syp	1.079221	0.0020913
Fam131a	1.045174	0.0279760
Lmna	1.044754	0.0000058
Dnm1	1.039805	0.0158126

4.1 Capillary marker: Pecam1

4.2 Capillary Cell Count

Since Pecam1 is capillary gene marker, we picked up endothelial cells that express log-normalized Pecam1 expression > 1, and consider them as capillary cells.

Capillary Cell Count

	id	cell.count
0	tBHP_4	743
3	tBHP_24	731
1	PBS_4	374
2	PBS_24	329

4.3 Defferentiation Volcano

4.3.1 Capillary, 4 hours, tBHP vs PBS

	logfoldchanges	pvals
Icam1	3.367107	0.0028161
Agt	-1.842217	0.0025396
Slc17a7	1.755432	0.0000049
Nnat	-1.531274	0.0000035
Klf2	-1.198818	0.0000029

4.3.2 Capillary, 24 hours, tBHP vs PBS

	logfoldchanges	pvals
Bsg	16.433660	0.0000000
Cldn5	11.126303	0.0000000
Apoe	5.104093	0.0000000
Camk2a	3.493571	0.0000000
App	3.254875	0.0000112
Flt1	2.968592	0.0000000
Mfsd2a	2.625379	0.0000000
Fn1	2.292427	0.0000043
Gfap	2.277436	0.0000160
Ctnnb1	2.137518	0.0000000
Pecam1	1.965661	0.0000000
Nos3	1.731574	0.0000000
Ntng2	1.706747	0.0411791
Klf2	1.691222	0.0000000
Trpm4	1.665571	0.0191938
Nptxr	1.616628	0.0000585
Syp	1.610862	0.0011809
Xdh	1.608494	0.0000000
Cx3cl1	1.570906	0.0000736
Cspg5	1.566026	0.0000017
Kcnq1	1.559081	0.0219258
Tcerg1	1.550006	0.0148341
Hpca	1.538213	0.0069025
Stard8	1.525962	0.0000401
Dnm1	1.466346	0.0031463
Lef1	1.389383	0.0000002
Rgs5	1.354013	0.0000014
Pdgfa	1.328179	0.0170938
Fam131a	1.322172	0.0439337
Rbfox3	1.271759	0.0134575
Eno2	1.252816	0.0177234
Mtor	1.234967	0.0002744
Erbb2	1.213557	0.0120796
Lmna	1.209302	0.0000229
Cdh5	1.195409	0.0000055
Bin1	1.182991	0.0031035
Zbtb20	1.168966	0.0000002
Grb2	1.167131	0.0043860
Plp1	1.156247	0.0058271
Syn1	1.093356	0.0075128
Adam10	1.042479	0.0035064

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic

ADP, anterodorsal preoptic nucleus

AHN, anterior hypothalamic nucleus

ARH, arcuate hypothalamic nucleus

CLI, central linear nucleus raphe

CUN, cuneiform nucleus

DMH, dorsomedial nucleus of the hypothalamus

DMX, dorsal motor nucleus of the vagus nerve

IF, interfascicular nucleus raphe

LHA, lateral hypothalamic area

MDRN, medullary reticular nucleus

MPN, medial preoptic nucleus

MPO, medial preoptic area

MV, medial vestibular nucleus

NTS, nucleus of the solitary tract

PAG, periaqueductal grey

PARN, parvicellular reticular nucleus

PB, parabrachial nucleus

PBG, parabigeminal nucleus

PGRN, paragigantocellular reticular nucleus

PGRNd, paragigantocellular reticular nucleus, dorsal part

PH, posterior hypothalamic nucleus

PMv, ventral premammillary nucleus

PPN, pedunculopontine nucleus

PVa, periventricular hypothalamic nucleus, anterior part

PVHd, paraventricular hypothalamic nucleus, descending division

PVi, periventricular hypothalamic nucleus, intermediate part

PVpo, periventricular hypothalamic nucleus, preoptic part

PVR, periventricular region

RAmb, midbrain raphe nuclei

RL, rostral linear nucleus raphe

SBPV, subparaventricular zone

SNc, substantia nigra, compact part

SPIV, spinal vestibular nucleus

TMv, tuberomammillary nucleus, ventral part

VII, facial motor nucleus

VMPO, ventromedial preoptic nucleus

VTA, ventral tegmental area

ZI, zona incerta.